1
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Wijker S, Palmans ARA. Protein-Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water. Chempluschem 2023; 88:e202300260. [PMID: 37417828 DOI: 10.1002/cplu.202300260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The folding of proteins into functional nanoparticles with defined 3D structures has inspired chemists to create simple synthetic systems mimicking protein properties. The folding of polymers into nanoparticles in water proceeds via different strategies, resulting in the global compaction of the polymer chain. Herein, we review the different methods available to control the conformation of synthetic polymers and collapse/fold them into structured, functional nanoparticles, such as hydrophobic collapse, supramolecular self-assembly, and covalent cross-linking. A comparison is made between the design principles of protein folding to synthetic polymer folding and the formation of structured nanocompartments in water, highlighting similarities and differences in design and function. We also focus on the importance of structure for functional stability and diverse applications in complex media and cellular environments.
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Affiliation(s)
- Stefan Wijker
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
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2
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Chullipalliyalil K, Elkassas K, McAuliffe MAP, Vucen S, Crean A. In-Vial Detection of Protein Denaturation Using Intrinsic Fluorescence Anisotropy. Anal Chem 2023; 95:2774-2782. [PMID: 36696963 PMCID: PMC9909669 DOI: 10.1021/acs.analchem.2c03912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The conventional quality control techniques for identifying the denaturation of biopharmaceuticals includes sodium dodecyl sulfate-polyacrylamide gel electrophoresis for identifying fragmentation, ion exchange chromatography and isoelectric focusing for identifying deamidation, reverse-phase high-performance liquid chromatography (HPLC) for identifying oxidation, and size-exclusion HPLC for identifying aggregation. These stability assessments require essential processes that are destructive to the product tested. All these techniques are lab based and require sample removal from a sealed storage vial, which can breach the sterility. In this work, we investigate the heat- and surfactant-induced denaturation of an in-vial-stored model protein, bovine serum albumin (BSA), by analyzing its intrinsic fluorescence without removing the sample from the vial. A lab-based bespoke setup which can do the measurement in vial is used to demonstrate the change in fluorescence polarization of the protein to determine the denaturation level. The results obtained are compared to circular dichroism and size-exclusion HPLC measurements. The results prove that in-vial fluorescence measurements can be performed to monitor protein denaturation. A cost-effective portable solution to provide a top-level overview of biopharmaceutical product stability from manufacture to the point of patient administration can be further developed using the same technique.
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Affiliation(s)
| | - Khaled Elkassas
- SSPC
Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, CorkT12 YT20, Ireland
| | - Michael A. P. McAuliffe
- Centre
for Advanced Photonics & Process Analysis, Munster Technological University Cork, CorkT12 P928, Ireland
| | - Sonja Vucen
- SSPC
Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, CorkT12 YT20, Ireland
| | - Abina Crean
- SSPC
Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, CorkT12 YT20, Ireland
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3
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The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy. Essays Biochem 2022; 66:875-890. [PMID: 36416865 PMCID: PMC9760427 DOI: 10.1042/ebc20220065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) have emerged as key players across many biological functions and diseases. Differently from structured proteins, disordered proteins lack stable structure and are particularly sensitive to changes in the surrounding environment. Investigation of disordered ensembles requires new approaches and concepts for quantifying conformations, dynamics, and interactions. Here, we provide a short description of the fundamental biophysical properties of disordered proteins as understood through the lens of single-molecule fluorescence observations. Single-molecule Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) provides an extensive and versatile toolbox for quantifying the characteristics of conformational distributions and the dynamics of disordered proteins across many different solution conditions, both in vitro and in living cells.
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4
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Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays Biochem 2021; 65:37-49. [PMID: 33600559 PMCID: PMC8052285 DOI: 10.1042/ebc20200022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/17/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022]
Abstract
The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole-dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).
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Affiliation(s)
- Joshua C Sanders
- Department of Chemistry, University of Kansas, Lawrence, KS, U.S.A
| | - Erik D Holmstrom
- Department of Chemistry, University of Kansas, Lawrence, KS, U.S.A
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, U.S.A
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5
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Jeanne Dit Fouque K, Fernandez-Lima F. Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. J Phys Chem B 2020; 124:6257-6265. [PMID: 32560586 PMCID: PMC8341290 DOI: 10.1021/acs.jpcb.0c04276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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6
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Abstract
Intrinsically disordered proteins (IDPs) are now widely recognized as playing critical roles in a broad range of cellular functions as well as being implicated in diverse diseases. Their lack of stable secondary structure and tertiary interactions, coupled with their sensitivity to measurement conditions, stymies many traditional structural biology approaches. Single-molecule Förster resonance energy transfer (smFRET) is now widely used to characterize the physicochemical properties of these proteins in isolation and is being increasingly applied to more complex assemblies and experimental environments. This review provides an overview of confocal diffusion-based smFRET as an experimental tool, including descriptions of instrumentation, data analysis, and protein labeling. Recent papers are discussed that illustrate the unique capability of smFRET to provide insight into aggregation-prone IDPs, protein–protein interactions involving IDPs, and IDPs in complex experimental milieus.
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Affiliation(s)
- Lauren Ann Metskas
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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7
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Birol M, Melo AM. Untangling the Conformational Polymorphism of Disordered Proteins Associated With Neurodegeneration at the Single-Molecule Level. Front Mol Neurosci 2020; 12:309. [PMID: 31998071 PMCID: PMC6965022 DOI: 10.3389/fnmol.2019.00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
A large fraction of the human genome encodes intrinsically disordered proteins/regions (IDPs/IDRs) that are involved in diverse cellular functions/regulation and dysfunctions. Moreover, several neurodegenerative disorders are associated with the pathological self-assembly of neuronal IDPs, including tau [Alzheimer's disease (AD)], α-synuclein [Parkinson's disease (PD)], and huntingtin exon 1 [Huntington's disease (HD)]. Therefore, there is an urgent and emerging clinical interest in understanding the physical and structural features of their functional and disease states. However, their biophysical characterization is inherently challenging by traditional ensemble techniques. First, unlike globular proteins, IDPs lack stable secondary/tertiary structures under physiological conditions and may interact with multiple and distinct biological partners, subsequently folding differentially, thus contributing to the conformational polymorphism. Second, amyloidogenic IDPs display a high aggregation propensity, undergoing complex heterogeneous self-assembly mechanisms. In this review article, we discuss the advantages of employing cutting-edge single-molecule fluorescence (SMF) techniques to characterize the conformational ensemble of three selected neuronal IDPs (huntingtin exon 1, tau, and α-synuclein). Specifically, we survey the versatility of these powerful approaches to describe their monomeric conformational ensemble under functional and aggregation-prone conditions, and binding to biological partners. Together, the information gained from these studies provides unique insights into the role of gain or loss of function of these disordered proteins in neurodegeneration, which may assist the development of new therapeutic molecules to prevent and treat these devastating human disorders.
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Affiliation(s)
- Melissa Birol
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Ana M Melo
- Centro de Química-Física Molecular- IN and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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8
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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9
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Xie S, Wong AYH, Chen S, Tang BZ. Fluorogenic Detection and Characterization of Proteins by Aggregation‐Induced Emission Methods. Chemistry 2019; 25:5824-5847. [DOI: 10.1002/chem.201805297] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Sheng Xie
- Ming Wai Lau Centre for Reparative MedicineKarolinska Institutet Hong Kong S.A.R. China
| | - Alex Y. H. Wong
- Ming Wai Lau Centre for Reparative MedicineKarolinska Institutet Hong Kong S.A.R. China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative MedicineKarolinska Institutet Hong Kong S.A.R. China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National, Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science, HKUST-Shenzhen Research InstituteThe Hong Kong University of Science and Technology, Kowloon Hong Kong S.A.R. China
- NSFC Center for Luminescence from Molecular AggregatesSCUT-HKUST Joint Research InstituteState Key Laboratory of Luminescent Materials and DevicesSouth China University of Technology Guangzhou 510640 P.R. China
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10
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LeBlanc SJ, Kulkarni P, Weninger KR. Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins. Biomolecules 2018; 8:biom8040140. [PMID: 30413085 PMCID: PMC6315554 DOI: 10.3390/biom8040140] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
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11
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Kuzishchin YA, Martynov IL, Osipov EV, Samokhvalov PS, Chistyakov AA, Nabiev IR. Comparison of fluorescence excitation modes for cdse semi-conductor quantum dots used in medical research. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2018. [DOI: 10.24075/brsmu.2018.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescence spectroscopy is a powerful tool used in applied biological and medical research. Colloid semi-conductor quantum dots are promising fluorescent tags for simultaneous detection of different biopathogens. The techniques employing these tags can be improved by selecting the optimal modes for signal excitation and detection. The aim of the present work was to derive a mathematical expression to describe the signal-to-noise ratios in the pulsed and modulated excitation modes. Below, we compare these two modes of fluorescence excitation in ultralow quantities of quantum dots. We demonstrate that modulated excitation should be preferred for CdSe/ZnS quantum dots given that signal accumulation time is over 100 mc and the photosensor is exposed to background light of > 1 μW.
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Affiliation(s)
- Y. A. Kuzishchin
- Department of Physics of Micro- and Nanosystems, National Research Nuclear University MEPhI, Moscow, Russia
| | - I. L. Martynov
- Department of Physics of Micro- and Nanosystems, National Research Nuclear University MEPhI, Moscow, Russia
| | - E. V. Osipov
- Department of Physics of Micro- and Nanosystems, National Research Nuclear University MEPhI, Moscow, Russia
| | - P. S. Samokhvalov
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI, Moscow, Russia
| | - A. A. Chistyakov
- Department of Physics of Micro- and Nanosystems, National Research Nuclear University MEPhI, Moscow, Russia
| | - I. R. Nabiev
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI, Moscow, Russia
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12
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The Characteristics of Intrinsic Fluorescence of Type I Collagen Influenced by Collagenase I. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8101947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The triple helix structure of collagen can be degraded by collagenase. In this study, we explored how the intrinsic fluorescence of type I collagen was influenced by collagenase I. We found that tyrosine was the main factor that could successfully excite the collagen fluorescence. Initially, self-assembly behavior of collagen resulted in a large amount of tyrosine wrapped with collagen, which decreased the fluorescence intensity of type I collagen. After collagenase cleavage, some wrapped-tyrosine could be exposed and thereby the intrinsic fluorescence intensity of collagen increased. By observation and analysis, the influence of collagenase to intrinsic fluorescence of collagen was investigated and elaborated. Furthermore, collagenase cleavage to the special triple helix structure of collagen would result in a slight improvement of collagen thermostability, which was explained by the increasing amount of terminal peptides. These results are helpful and effective for reaction mechanism research related to collagen, which can be observed by fluorescent technology. Meantime, the reaction behaviors of both collagenase and collagenolytic proteases can also be analyzed by fluorescent technology. In conclusion, this research provides a foundation for the further investigation of collagen reactions in different areas, such as medicine, nutrition, food and agriculture.
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13
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Fluorescence self-quenching assay for the detection of target collagen sequences using a short probe peptide. Talanta 2018; 176:492-498. [DOI: 10.1016/j.talanta.2017.08.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/27/2017] [Accepted: 08/11/2017] [Indexed: 01/05/2023]
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14
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Melo AM, Elbaum-Garfinkle S, Rhoades E. Insights into tau function and dysfunction through single-molecule fluorescence. Methods Cell Biol 2017; 141:27-44. [PMID: 28882307 DOI: 10.1016/bs.mcb.2017.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescence correlation spectroscopy and single-molecule Förster resonance energy transfer are powerful and versatile techniques to quantify and describe molecular interactions. They are particularly well suited to the study of dynamic proteins and assemblies, as they can overcome some of the challenges that stymie more conventional ensemble approaches. In this chapter, we describe the application of these methods to study the interaction of tau with the molecular aggregation inducer, heparin, and the functional binding partner, soluble tubulin. Specifically, we outline the practical aspects of both techniques to characterize the critical first steps of tau aggregation and tau-mediated microtubule polymerization. The information gained from these measurements provides unique insight into tau function and its role in disease.
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Affiliation(s)
- Ana M Melo
- University of Pennsylvania, Philadelphia, PA, United States
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15
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Krainer G, Gracia P, Frotscher E, Hartmann A, Gröger P, Keller S, Schlierf M. Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A. Biophys J 2017. [PMID: 28629619 DOI: 10.1016/j.bpj.2017.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Structural and dynamic investigations of unfolded proteins are important for understanding protein-folding mechanisms as well as the interactions of unfolded polypeptide chains with other cell components. In the case of outer-membrane proteins (OMPs), unfolded-state properties are of particular physiological relevance, because these proteins remain unfolded for extended periods of time during their biogenesis and rely on interactions with binding partners to support proper folding. Using a combination of ensemble and single-molecule spectroscopy, we have scrutinized the unfolded state of outer-membrane phospholipase A (OmpLA) to provide a detailed view of its structural dynamics on timescales from nanoseconds to milliseconds. We find that even under strongly denaturing conditions and in the absence of residual secondary structure, OmpLA populates an ensemble of slowly (>100 ms) interconverting and conformationally heterogeneous unfolded states that lack the fast chain-reconfiguration motions expected for an unstructured, fully unfolded chain. The drastically slowed sampling of potentially folding-competent states, as compared with a random-coil polypeptide, may contribute to the slow in vitro folding kinetics observed for many OMPs. In vivo, however, slow intramolecular long-range dynamics might be advantageous for entropically favored binding of unfolded OMPs to chaperones and, by facilitating conformational selection after release from chaperones, for preserving binding-competent conformations before insertion into the outer membrane.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany; Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Pablo Gracia
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Erik Frotscher
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Philip Gröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany.
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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16
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17
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Zabik NL, Imhof MM, Martic-Milne S. Structural evaluations of tau protein conformation: methodologies and approaches. Biochem Cell Biol 2017; 95:338-349. [PMID: 28278386 DOI: 10.1139/bcb-2016-0227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Protein-misfolding diseases are based on a common principle of aggregation initiated by intra- and inter-molecular contacts. The structural and conformational changes induced by biochemical transformations such as post-translational modifications (PTMs), often lead to protein unfolding and misfolding. Thus, these order-to-disorder or disorder-to-order transitions may regulate cellular function. Tau, a neuronal protein, regulates microtubule (MT) structure and overall cellular integrity. However, misfolded tau modified by PTMs results in MT destabilization, toxic tau aggregate formation, and ultimately cell death, leading to neurodegeneration. Currently, the lack of structural information surrounding tau severely limits understanding of neurodegeneration. This minireview focuses on the current methodologies and approaches aimed at probing tau conformation and the role of conformation in various aspects of tau biochemistry. The recent applications of nuclear magnetic resonance, mass spectrometry, Förster resonance electron transfer, and molecular dynamics simulations toward structural analysis of conformational landscapes of tau will be described. The strategies developed for structural evaluation of tau may significantly improve our understanding of misfolding diseases.
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Affiliation(s)
- Nicole L Zabik
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.,Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Matthew M Imhof
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.,Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Sanela Martic-Milne
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.,Department of Chemistry, Oakland University, Rochester, MI 48309, USA
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18
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Schuler B, Soranno A, Hofmann H, Nettels D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys 2016; 45:207-31. [PMID: 27145874 DOI: 10.1146/annurev-biophys-062215-010915] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
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19
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Sun X, Fan J, Li X, Zhang S, Liu X, Xiao J. Colorimetric and fluorometric monitoring of the helix composition of collagen-like peptides at the nM level. Chem Commun (Camb) 2016; 52:3107-10. [PMID: 26692232 DOI: 10.1039/c5cc09565d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have demonstrated that the incorporation of a dye-labeled collagen-like peptide in the homotrimeric versus heterotrimeric context results in visible color changes and distinct fluorescence. The unique fluorescence self-quenching assay can unambiguously determine the helix composition of heterotrimers at the nM level, far extending our capability to characterize a collagen triple helix.
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Affiliation(s)
- Xiuxia Sun
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Jun Fan
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Xuan Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Shanshan Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Xiaoyan Liu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Jianxi Xiao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
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20
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Microsecond protein dynamics observed at the single-molecule level. Nat Commun 2015; 6:7685. [PMID: 26151767 PMCID: PMC4506535 DOI: 10.1038/ncomms8685] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/01/2015] [Indexed: 01/27/2023] Open
Abstract
How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. Single molecule spectroscopy can visualise dynamic changes in protein conformation on the submillisecond timescale. Here, Otosu et al. apply two-dimensional fluorescence lifetime correlation spectroscopy to visualise dynamics between seven conformers of cytochrome c on the microsecond timescale.
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22
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Walsh G. Protein Purification and Characterization. Proteins 2015. [DOI: 10.1002/9781119117599.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Lee AJ, Asher WB, Stern HA, Bren KL, Krauss TD. Single-Molecule Analysis of Cytochrome c Folding by Monitoring the Lifetime of an Attached Fluorescent Probe. J Phys Chem Lett 2013; 4:2727-2733. [PMID: 24116268 PMCID: PMC3791595 DOI: 10.1021/jz401259y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Conformational dynamics of proteins are important for function. However, obtaining information about specific conformations is difficult for samples displaying heterogeneity. Here, time-resolved fluorescence resonance energy transfer is used to characterize the folding of single cytochrome c molecules. In particular, measurements of the fluorescence lifetimes of individual cytochrome c molecules labeled with a single dye that is quenched by energy transfer to the heme were used to monitor conformational transitions of the protein under partially denaturing conditions. These studies indicate significantly more conformational heterogeneity than has been described previously. Importantly, the use of a purified singly-labeled sample made a direct comparison to ensemble data possible. The distribution of lifetimes of single-proteins was compared to the distribution of lifetimes determined from analysis of ensemble lifetime fluorescence data. The results show broad agreement between single-molecule and ensemble data, with a similar range of lifetimes. However, the single-molecule data reveal greater conformational heterogeneity.
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24
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Nath A, Sammalkorpi M, DeWitt DC, Trexler AJ, Elbaum-Garfinkle S, O'Hern CS, Rhoades E. The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulations. Biophys J 2013. [PMID: 23199922 DOI: 10.1016/j.bpj.2012.09.032] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are increasingly recognized for their important roles in a range of biological contexts, both in normal physiological function and in a variety of devastating human diseases. However, their structural characterization by traditional biophysical methods, for the purposes of understanding their function and dysfunction, has proved challenging. Here, we investigate the model IDPs α-Synuclein (αS) and tau, that are involved in major neurodegenerative conditions including Parkinson's and Alzheimer's diseases, using excluded volume Monte Carlo simulations constrained by pairwise distance distributions from single-molecule fluorescence measurements. Using this, to our knowledge, novel approach we find that a relatively small number of intermolecular distance constraints are sufficient to accurately determine the dimensions and polymer conformational statistics of αS and tau in solution. Moreover, this method can detect local changes in αS and tau conformations that correlate with enhanced aggregation. Constrained Monte Carlo simulations produce ensembles that are in excellent agreement both with experimental measurements on αS and tau and with all-atom, explicit solvent molecular dynamics simulations of αS, with much lower configurational sampling requirements and computational expense.
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Affiliation(s)
- Abhinav Nath
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
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25
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Nath A, Rhoades E. A flash in the pan: dissecting dynamic amyloid intermediates using fluorescence. FEBS Lett 2013; 587:1096-105. [PMID: 23458258 DOI: 10.1016/j.febslet.2013.02.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 12/15/2022]
Abstract
Several widespread and severe degenerative diseases are characterized by the deposition of amyloid protein aggregates in affected tissues. While there is great interest in the complete description of the aggregation pathway of the proteins involved, a molecular level understanding is hindered by the complexity of the self-assembly process. In particular, the early stages of aggregation, where dynamic, heterogeneous and often toxic intermediates are populated, are resistant to high-resolution structural characterization. Fluorescence spectroscopy is a powerful and versatile tool for such analysis. In this review, we survey its application to provide residue-specific information about amyloid intermediate states for three selected proteins: IAPP, α-synuclein, and tau.
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Affiliation(s)
- Abhinav Nath
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
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26
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Trexler AJ, Rhoades E. Function and dysfunction of α-synuclein: probing conformational changes and aggregation by single molecule fluorescence. Mol Neurobiol 2012; 47:622-31. [PMID: 22983916 DOI: 10.1007/s12035-012-8338-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 08/19/2012] [Indexed: 01/21/2023]
Abstract
The aggregation and deposition of the neuronal protein α-synuclein in the substantia nigra region of the brain is a key pathological feature of Parkinson's disease. α-Synuclein assembles from a monomeric state in solution, which lacks stable secondary and tertiary contacts, into highly structured fibrillar aggregates through a pathway which involves the population of multiple oligomeric species over a range of time scales. These features make α-synuclein well suited for study with single-molecule techniques, which are particularly useful for characterizing dynamic, heterogeneous samples. Here, we review the current literature featuring single-molecule fluorescence studies of α-synuclein and discuss how these studies have contributed to our understanding of both its function and its role in disease.
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Affiliation(s)
- Adam J Trexler
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P.O. Box 208114, New Haven, CT 06511, USA
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27
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Immobilization of proteins for single-molecule fluorescence resonance energy transfer measurements of conformation and dynamics. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 896:3-20. [PMID: 22821514 DOI: 10.1007/978-1-4614-3704-8_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence resonance energy transfer provides information about protein structure and dynamics. Single-molecule analysis can capture the information normally lost through ensemble averaging of heterogeneous and dynamic samples. Immobilization of single molecules, under conditions that retain their biological activity, allows for extended observation of the same molecule for tens of seconds. This can capture slow conformational transitions or protein binding and unbinding cycles. Using an open geometry for immobilization allows for direct observation of the response to changing solution conditions or adding ligands. Here we provide detailed methods for immobilization and observation of fluorescently labeled single proteins using total internal reflection microscopy that are widely applicable to the study of intrinsically disordered proteins.
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28
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Haran G. How, when and why proteins collapse: the relation to folding. Curr Opin Struct Biol 2011; 22:14-20. [PMID: 22104965 DOI: 10.1016/j.sbi.2011.10.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/15/2011] [Accepted: 10/18/2011] [Indexed: 11/25/2022]
Abstract
Unfolded proteins under strongly denaturing conditions are highly expanded. However, when the conditions are more close to native, an unfolded protein may collapse to a compact globular structure distinct from the folded state. This transition is akin to the coil-globule transition of homopolymers. Single-molecule FRET experiments have been particularly conducive in revealing the collapsed state under conditions of coexistence with the folded state. The collapse can be even more readily observed in natively unfolded proteins. Time-resolved studies, using FRET and small-angle scattering, have shown that the collapse transition is a very fast event, probably occurring on the submicrosecond time scale. The forces driving collapse are likely to involve both hydrophobic and backbone interactions. The loss of configurational entropy during collapse makes the unfolded state less stable compared to the folded state, thus facilitating folding.
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Affiliation(s)
- Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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Choi UB, McCann JJ, Weninger KR, Bowen ME. Beyond the random coil: stochastic conformational switching in intrinsically disordered proteins. Structure 2011; 19:566-76. [PMID: 21481779 DOI: 10.1016/j.str.2011.01.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 01/21/2011] [Accepted: 01/26/2011] [Indexed: 01/24/2023]
Abstract
Intrinsically disordered proteins (IDPs) participate in critical cellular functions that exploit the flexibility and rapid conformational fluctuations of their native state. Limited information about the native state of IDPs can be gained by the averaging over many heterogeneous molecules that is unavoidable in ensemble approaches. We used single molecule fluorescence to characterize native state conformational dynamics in five synaptic proteins confirmed to be disordered by other techniques. For three of the proteins, SNAP-25, synaptobrevin and complexin, their conformational dynamics could be described with a simple semiflexible polymer model. Surprisingly, two proteins, neuroligin and the NMDAR-2B glutamate receptor, were observed to stochastically switch among distinct conformational states despite the fact that they appeared intrinsically disordered by other measures. The hop-like intramolecular diffusion found in these proteins is suggested to define a class of functionality previously unrecognized for IDPs.
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Affiliation(s)
- Ucheor B Choi
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
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30
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Huang Y, Liu Z. Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein. Int J Mol Sci 2011; 12:1410-30. [PMID: 21541066 PMCID: PMC3083713 DOI: 10.3390/ijms12021410] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/10/2011] [Accepted: 02/16/2011] [Indexed: 02/03/2023] Open
Abstract
Anchor residues, which are deeply buried upon binding, play an important role in protein–protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs) which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17–Asn29, abbreviated as p53N) which are involved in binding with two different targets (MDM2 and Taz2), and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex). We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs).
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Affiliation(s)
- Yongqi Huang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Theoretical Biology, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhirong Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Theoretical Biology, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-10-62753422; Fax: +86-10-62751708
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31
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Single molecule characterization of α-synuclein in aggregation-prone states. Biophys J 2011; 99:3048-55. [PMID: 21044603 DOI: 10.1016/j.bpj.2010.08.056] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 08/23/2010] [Accepted: 08/27/2010] [Indexed: 01/17/2023] Open
Abstract
α-Synuclein (αS) is an intrinsically disordered protein whose aggregation into ordered, fibrillar structures underlies the pathogenesis of Parkinson's disease. A full understanding of the factors that cause its conversion from soluble protein to insoluble aggregate requires characterization of the conformations of the monomer protein under conditions that favor aggregation. Here we use single molecule Förster resonance energy transfer to probe the structure of several aggregation-prone states of αS. Both low pH and charged molecules have been shown to accelerate the aggregation of αS and induce conformational changes in the protein. We find that at low pH, the C-terminus of αS undergoes substantial collapse, with minimal effect on the N-terminus and central region. The proximity of the N- and C-termini and the global dimensions of the protein are relatively unaffected by the C-terminal collapse. Moreover, although compact at low pH, with restricted chain motion, the structure of the C-terminus appears to be random. Low pH has a dramatically different effect on αS structure than the molecular aggregation inducers spermine and heparin. Binding of these molecules gives rise to only minor conformational changes in αS, suggesting that their mechanism of aggregation enhancement is fundamentally different from that of low pH.
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32
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Rosenkranz T, Schlesinger R, Gabba M, Fitter J. Native and Unfolded States of Phosphoglycerate Kinase Studied by Single‐Molecule FRET. Chemphyschem 2010; 12:704-10. [DOI: 10.1002/cphc.201000701] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 09/29/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Tobias Rosenkranz
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Ramona Schlesinger
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Matteo Gabba
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Jörg Fitter
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
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33
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Kulzer F, Xia T, Orrit M. Einzelmoleküle als optische Nanosonden für weiche und komplexe Materie. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904858] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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34
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Kulzer F, Xia T, Orrit M. Single Molecules as Optical Nanoprobes for Soft and Complex Matter. Angew Chem Int Ed Engl 2010; 49:854-66. [PMID: 20052698 DOI: 10.1002/anie.200904858] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Kulzer
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
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35
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Makarov DE, Plaxco KW. Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency. J Chem Phys 2009; 131:085105. [PMID: 19725638 PMCID: PMC2754924 DOI: 10.1063/1.3212602] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 08/04/2009] [Indexed: 11/14/2022] Open
Abstract
Recent years have seen a number of investigations in which distances within unfolded proteins, polypeptides, and other biopolymers are probed via fluorescence resonance energy transfer, a method that relies on the strong distance dependence of energy transfer between a pair of dyes attached to the molecule of interest. In order to interpret the results of such experiments it is commonly assumed that intramolecular diffusion is negligible during the excited state lifetime. Here we explore the conditions under which this "frozen chain" approximation fails, leading to significantly underestimated donor-acceptor distances, and describe a means of correcting for polymer dynamics in order to estimate these distances more accurately.
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Affiliation(s)
- Dmitrii E Makarov
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.
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36
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Eliezer D. Biophysical characterization of intrinsically disordered proteins. Curr Opin Struct Biol 2009; 19:23-30. [PMID: 19162471 DOI: 10.1016/j.sbi.2008.12.004] [Citation(s) in RCA: 252] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Accepted: 12/04/2008] [Indexed: 10/21/2022]
Abstract
The challenges associated with the structural characterization of disordered proteins have resulted in the application of a host of biophysical methods to such systems. NMR spectroscopy is perhaps the most readily suited technique for providing high-resolution structural information on disordered protein states in solution. Optical methods, solid state NMR, ESR and X-ray scattering can also provide valuable information regarding the ensemble of conformations sampled by disordered states. Finally, computational studies have begun to assume an increasingly important role in interpreting and extending the impact of experimental data obtained for such systems. This article discusses recent advances in the applications of these methods to intrinsically disordered proteins.
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Affiliation(s)
- David Eliezer
- Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, United States.
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